January 2025
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41 Reads
Genome Biology and Evolution
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January 2025
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41 Reads
Genome Biology and Evolution
January 2025
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199 Reads
Science
How populations adapt to their environment is a fundamental question in biology. Yet, we know surprisingly little about this process, especially for endangered species, such as nonhuman great apes. Chimpanzees, our closest living relatives, are particularly notable because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite it having wide implications for evolutionary biology and conservation. By using newly sequenced exomes from 828 wild chimpanzees (388 postfiltering), we found evidence of fine-scale genetic adaptation to habitat, with signatures of positive selection in forest chimpanzees in the same genes underlying adaptation to malaria in humans. This work demonstrates the power of noninvasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.
December 2024
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283 Reads
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1 Citation
Nature Ecology & Evolution
Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.
November 2024
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117 Reads
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1 Citation
Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource for studying the evolution of DNA viruses. Their genetic material is likely to be preserved in dry museum specimens, as reported previously for monkeypox virus genomes from historical orangutan specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We determined the presence of multiple viruses within this dataset from historical specimens and obtained several near-complete viral genomes. In particular, we report high-coverage (> 18-fold) hepatitis B virus genomes from one gorilla and two chimpanzee individuals, which are phylogenetically placed within clades infecting the respective host species.
October 2024
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188 Reads
Communications Biology
Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest’s dynamism on wild primates’ genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.
October 2024
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184 Reads
eLife
The Xerces Blue ( Glaucopsyche xerces ) is considered to be the first butterfly to become extinct in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. We sequenced the genomes of four 80- to 100-year-old Xerces Blue, and seven historical and one modern specimens of its closest relative, the Silvery Blue ( Glaucopsyche lygdamus ). We compared these to a novel annotated genome of the Green-Underside Blue ( Glaucopsyche alexis ). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, both species experienced population growth during the Eemian interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity and deleterious load in the former were significantly greater than in the later, suggesting a higher incidence of inbreeding. These signals of population decline observed in Xerces Blue could be used to identify and monitor other insects threatened by human activities, whose extinction patterns are still not well known.
July 2024
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330 Reads
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2 Citations
How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees. One-Sentence Summary Chimpanzees show evidence of local genetic adaptation to habitat, particularly to pathogens, such as malaria, in forests.
April 2024
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75 Reads
Natural history museum collections harbour a record of wild species from the past centuries, providing a unique opportunity to study animals as well as their infectious agents. Thousands of great ape specimens are kept in these collections, and could become an important resource to study the evolution of DNA viruses, whose genetic material is likely to be preserved in dry museum specimens. Here, we screened 209 great ape museum specimens for 99 different DNA viruses, using hybridization capture coupled with short-read high-throughput sequencing. We report a capture design for great ape DNA viruses, sequencing data obtained using this approach, as well as findings regarding the presence of viruses, and several viral genomes obtained from historical specimens.
February 2024
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234 Reads
Ancient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil specimens and to estimate divergence times. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentation post mortem. Moreover, some of the enamelome genes are paralogous or may coevolve. This raises the question as to whether the enamelome provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments (MSAs) for each protein and estimated the evolutionary rate for each site and examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1-2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We found that the composition of the proteome influences the phylogenetic placement of Tarsiiformes. For the inference of molecular phylogenies based on paleoproteomic data, we recommend characterizing the evolution of the proteomes from the closest extant relatives to maximize the reliability of phylogenetic inference.
January 2024
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94 Reads
The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct at global scale in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last individuals were collected in their restricted habitat, in the dunes near the Presidio military base in San Francisco, in 1941. To explore the demographic history of this iconic butterfly and to better understand why it went extinct, we sequenced at medium coverage the genomes of four 80 to 100-year-old Xerces Blue specimens and seven historic specimens of its closest relative, the Silvery Blue (G. lygdamus). We compared these to a novel annotated genome of the Green-Underside Blue (G. alexis). Phylogenetic relationships inferred from complete mitochondrial genomes indicate that Xerces Blue was a distinct species that diverged from the Silvery Blue lineage at least 850,000 years ago. Using nuclear genomes, we show that both species experienced population growth during the MIS 7 interglacial period, but the Xerces Blue decreased to a very low effective population size subsequently, a trend opposite to that observed in the Silvery Blue. Runs of homozygosity in the Xerces Blue were significantly greater than in the Silvery Blue, suggesting a higher incidence of inbreeding. In addition, the Xerces Blue carried a higher proportion of derived, putatively deleterious amino acid-changing alleles than the Silvery Blue. These results demonstrate that the Xerces Blue experienced more than 100 thousand years of population decline, prior to its human-induced final extinction.
... We repeated the phasing analysis with POOHA on the baboons sequenced in our study and those from Wu and colleagues [12], enabling us to assign 49.3% (256/519) of mutations as being transmitted by one parent or the other (Tables 2 and S3). The higher level of overall nucleotide polymorphism in baboons gave us more power to phase mutations in this species compared to aye-ayes, which have a low level of polymorphism even for strepsirrhines [25,33]. Based on the percentage of mutations that could be phased in each trio, we inferred the number of mutations that each parent transmitted to their offspring. ...
December 2024
Nature Ecology & Evolution
... can track long-term trends in their parasite communities and even test hypotheses about drivers such as climate change 71,200,201 . Preserved tissues can also be used to discover uncharacterized pathogens, including from species that are otherwise hard to sample (for example, rare and endangered species) 202,203 (Fig. 4b). ...
Reference:
Pathogens and planetary change
November 2024
... In a more comprehensive manner, Fontsere et al. (2022) 39 captured chimpanzee chromosome 21 sequences from 828 noninvasive samples collected at 48 research sites, revealing four distinct subspecies with local population structures across Africa. Furthermore, a recent preprint reported that exome sequences from these 828 samples to analyze fine-scale genetic adaptation to habitat 40 . ...
July 2024
... We looked for variants in the 219 candidate genes in two datasets. To find aye-aye and lemuriform-specific substitutions, we extracted 239 primate species from the 447-way whole-genome multiple sequence alignments in Kuderna and colleagues [65]. Alignment data from aye-aye, 30 lemur species, and 7 sifaka species were downloaded as MAF files. ...
November 2023
Nature
... Cave (Cortada & Maroto, 1990;, Cova del Gegant (Daura et al., 2005;Quam et al., 2015), Cova Simanya (Morales et al., 2023), Tossal de la Font (Olaria et al., 2004(Olaria et al., -2005, Cova Negra (Arsuaga et al., 2007;Richard et al., 2019), Cova Foradà (Aparicio et al., 2014;Subirà et al., 2003), El Salt (Garralda et al., 2014), Cova Bolomor (Arsuaga et al., 2001, Sima de las Palomas (Trinkaus & Walker, 2017;Walker et al., 2011Walker et al., , 2012Walker, Lombardi, et al., 2010), Boquete de Zafarraya (García Sánchez, 1986), and Gibraltar Caves (Bokelmann et al., 2019;Finlayson et al., 2006). The sites of Cova Bolomor dated around 120 kyr BP, and Sima de las Palomas, dated between 128 and 60 kyr BP, have yielded some of the oldest Neanderthal remains of the Iberian Peninsula (Arsuaga et al., 2001Walker et al., 2011Walker et al., , 2012Walker, Lombardi, et al., 2010). ...
September 2023
... Using these methods, it is possible to determine whether populations have suffered the deleterious effects of population declines and to assess the need for and feasibility of specific measures to restore their level of diversity, for example, using genetic rescue (Frankham, 2015). These methods have also been used to investigate the genomic signals of population decline leading to the extinction of the Xerces Blue butterfly, Glaucopsyche xerces (De-Dios et al., 2023). Screening for such signals might be very useful to detect and prevent future extinctions. ...
July 2023
... These traits could be used to identify other remains belonging to P. capensis, but a revision of the southern African paleoanthropological assemblages would be needed beforehand as it is too premature to formally assign other specimens to the hypodigm for now. However, a recent paleoproteomic analysis revealed a high degree of morphological and proteomic variation among four Paranthropus dental specimens from the 2-Ma Member 1 of Swartkrans, suggesting based on the absence of AMELY proteins that some of the largest teeth likely belong to female individuals, whereas smaller ones (like SK 835) are males and hinting at the possible presence of two species within the sample (Madupe et al., 2023). The M 3 SK 835 shows smaller dimensions (Dean et al., 2020) and a different shape of the EDJ than most specimens from Swartkrans and TM 1517, the holotype of P. robustus. ...
July 2023
... AI models like AlphaMissense and PrimateAI-3D have demonstrated remarkable capabilities in predicting the pathogenicity of genetic variants based on structure and function of proteins and evolutionary conservation [33,34]. AlphaMissense is a deep learning model that leverages protein structural information and evolutionary constraints from related sequences to accurately classify genetic variants as benign or pathogenic [33]. ...
June 2023
Science
... Ayeayes also have a long life span relative to their body size, in some cases living more than 30 years and reproducing at much older ages than other lemuriforms [23]. Their distinctive morphology and behavior have evolved through an extensive period of evolutionary independence: D. madagascariensis is the only extant member of the Daubentoniidae primate family and is estimated to have diverged from all other Malagasy lemurs at least 50 million years ago [24,25]. ...
June 2023
Science
... ,42 . Targeting species in key primate groups to assemble Y chromosome references ...
May 2023